Amorphous carbon is a material that is finding increasing usage in semiconductor processing. It is a particularly useful as a hardmask type material because of the nearly vertical sidewalls obtainable with this material. Additionally, high aspect ratios can be obtained using amorphous carbon layers. Additionally, amorphous carbon material is attractive because it can be formed into highly versatile etch stop layers. Accordingly, amorphous carbon layers (a-CL) have found wide acceptance and increasing utility in the semiconductor processing. Additionally, a-CL's find wide usage in many different layers of semiconductor manufacture. This includes the fabrication of overlay targets. Overlay targets are used for, among other things, determining the alignment of various layers of semiconductor substrates. These overlay targets are used in overlay metrology processes known to those having ordinary skill in the art. Overlay metrology is generally performed using bright field high magnification imaging or broadband spectroscopy or spectroscopic ellipsometry or scatterometry of metrology structures generated by semiconductor manufacturing patterning processes. Although suitable for their intended purposes, such approaches have certain limitations when used in conjunction with a-CL's. One of the difficulties is that imaging through a-CL's with visible light may lead to significant attenuation resulting in metrology performance degradation. In conducting overlay metrology using only visible light the presence of a-CL and other opaque (in the visible range) materials have caused a number of problems which the presently claimed inventive embodiments seek to remedy. The inventors have sought for and discovered new approaches for conducting metrology through amorphous carbon layers.